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Duccio Cavalieri phD.
Researcher and Professor of Microbiology.
Current Address:Computational Biology
Research and Innovation Centre – Fondazione Edmund Mach
Via E. Mach 1, 38010 – S. Michele all’Adige (TN), Italia
Tel +39 0461 615 153
e-mail: duccio.cavalieri@iasma.it
Web Page:
http://www.duccioknights.org/
Research Interests
The principal research interest of Duccio Cavalieri is Microbial Systems Biology. As a consequence Cavalieri’s research combines both wet lab projects and “in silico” bioinformatics projects. The Cavalieri’s laboratory is currently an interdisciplinary effort of 8 researchers, 3 biologists (one phD student and two undergraduates) and 5 bioinformaticians (3 postdoctoral fellows, one IT person and one database curator), and interacts actively with a company of 2 professional programmers, Inspect. It.
Dr. Cavalieri’s recent research has focused mainly on the following subjects.
1-Evolutionary and environmental comparative genomics. We are investigating how genetic diversity is generated and maintained, and how it affects the populations in laboratory and natural settings with particular attention to how sensing of environmental stimuli affects cell signalling and metabolic shifts.
The interest in studies on population genetics of yeast has grown since 1993, when these studies were initiated during his undergraduate work with Mario Dr. Polsinelli, in collaboration with Dr. Robert Mortimer (UC Berkeley), recipient of the 2003 Beadle Medal of Genetics for his revolutionary work in yeast genetics. These studies have progressed substantially with subsequent application of microarray-based whole genome technologies pioneered by Cavalieri since his arrival in Dr. Daniel Hartl’s laboratory in 1999. The results achieved by our group in this field have been seminal to the application of array based technologies in population genetics.
Cavalieri’s research has shown extensive heterozygotic variation within a single wild strain, between wild strains, and between wild and lab strains in different and ecologically relevant environmental conditions. The genetic determinants underlying this variation have been mapped to regulators of mitochondrial metabolism, and sensors of extracellular aminoacids.
These studies are now integrating expression modules and metabolic networks with fitness at different temperatures and in different environments, in quest for new master regulators of cellular metabolism.
Our studies applying systems biology approach to the study of life at zero degrees, in collaboration with Alfred Goldberg, Harvard Medical School, have indicated novel mechanisms of the adaptation of yeast cells to life at extreme temperatures, underlying the importance of temperature in yeast ecology and evolution.
Upon expanding his research from population genetics to ecological-genomics, Dr. Cavalieri has recently obtained promising results in studies investigating yeast’s ability to adapt to stresses found in its natural environment, such as fatty acids, acetic acid and ethanol and the role of resveratrol in the modulation of the response to high levels of these compounds.
In particular we are proposing that the observation that resveratrol extends life span mimicking caloric restriction is due to a mechanism of physiologic adaptation to mild oxidative stress.
2-Yeast as a model in Nutritional Systems Biology. We propose yeast as a model in comparative Nutrigenomics and Toxicogenomics. In particular we are addressing the connection between diet, balance between respiration and fermentation and reactive oxygen species levels. We are convinced that understanding mechanisms evolved in wine yeasts to adapt to and resist resveratrol and other phitoalexins, high fat levels, osmotic shock, and ethanol and acetic acid stress will likely prove important in understanding strategies that mammalian cells use to cope with ROS overload.
3-Dendritic cells -yeast interaction and pathways. Our research aims at using a systems biology and comparative genomics approach to dissect the specificity of response of dendritic cells to microrganisms. trying to detect genes expressed specifically in response to pathogens. To this aim we propose experiments to investigate the response of dendritic cells to pathogenic and non pathogenic yeasts on a whole genome scale, and development of algorithms and software for the integration of the expression data with protein protein interaction networks, existing biological information and interpretation of the results in the context of the evolution of the host-pathogen interaction in the different systems analyzed.
Our group is also working at establishing the methodological bases and developing the computational infrastructures to investigate the networks of molecular interactions characterizing specific DC differentiation programs. The methodological aim of the project is to develop a repository of pathways and genomics datasets regarding DC’s and algorithms for the integrative analysis of high-throughput molecular data in the light of the structural and functional organization of the genome. These computational methods will contribute fulfilling gaps in the bioinformatics analysis of genomic data where the integration of different types of information still represent a major, and partially unresolved, computational issue. The analytical results will support the reconstruction of regulatory networks and the molecular signatures of DC maturation. Strategically, the project has the objective to create an interdisciplinary research group integrating biological, bioinformatics and statistical expertise which will guarantee the development of a systemic approach to decipher the complex biological system behind DC maturation and the immune response.
4-Systems Biology approaches to the development of new antifungals-Fungal infections are increasing significantly in general and can have serious consequences in immunocompromised patients, in patients heavily treated with antibiotics. Currently only a limited number of antifungal drugs are available all targeted to the cell wall. We are working in collaboration with organic chemists and biochemists to testing new antifungal agents, such as peptides, esculentin, or agents improving the recognition of the fungal pathogen by the immune system. Our approaches are based on the modelling of yeast cell wall and small molecule transport networks, integrating data from competition experiments using the yeast deletion collection, functional assays based on DNA microarrays and proteomics.
5-Bioinformatics: Since 2000 Cavalieri’s group has had a special focus in comparative parallel analysis of large datasets in particular gene expression microarray data. His research proposes novel approaches to the understanding of genomics data.
Given the statistical limitations for assessment of significance at the gene level in microarray data, Cavalieri’s group has pioneered the application of group testing methods and methods for pathway based analysis and module reconstruction.
Regulation of gene expression and protein activity is central to the function of molecular and cellular systems. High throughput methods provide various partial views of the participating genes, RNAs and proteins, and their interactions.
Genes never act alone in a biological system, but participate in a cascade of networks. Pathways represent the biologist’s way of describing the nature of biological interactions and control networks.
Integration of “omics” data in the context of the biological and cellular pathways is particularly relevant for the detection of subtle but co-ordinated changes (Cavalieri D and De Filippo C., Bioinformatic Methods for Integrating Whole-Genome Expression Results into Cellular Networks. may 2005 Drug Discovery Today). A major direction of Dr. Cavalieri’s lab is bioinformatics and systems biology. In extracting the crucial data from microarray experiments, we have not only studied and used the most significant of currently available genomic tools. We have also developed additional innovative Bioinformatic methods (Pathway Processor and EuGene) to analyse expression data according to a pathway-based logic, which in addition indicates the statistical significance of the conclusions and provides user-friendly graphics to map the expression variability of metabolic pathways. Dr. Cavalieri is currently trying to predict the output of metabolic fluxes in these conditions and measure enzyme activities and metabolite levels in order to tackle variation on the level of systems biology.
The integration of pathway information with network reconstruction is studied in the cellular context, integrating the feedback loops of metabolites on the transcriptional regulators on the binding of transcription factors or their possibility to switch function, from activators, to repressors, binding to a metabolite-small molecule.
Cavalieri’s group is leading an initiative named i-Atlas, a curated database of Immunology signalling pathways in particular for the dendritic cell (DC-Base), the initiative is funded by the EU in the 7th framework programme.
Cavalieri’s group has been and is currently involved in the reconstruction of Colon Cancer modules to develop predictive markers of outcome at the pathway level, project funded by the Istituto Toscano Tumori Led by Lucio Luzzatto.
Cavalieri’s group is also involved in the construction of thematic microarray databases for nutrition (NUGO EU in the 6th framework programme), immunology(DC Thera EU in the 6th framework programme), and paediatric tumours (Cassa di Risparmio e associazione Noi Per Voi Meyer’s Hospital), and in the development of tools to interrogate these databases.
Previous Interests
During his previous research, Dr. Cavalieri has acquired fundamental knowledge in yeast genetics, molecular biology and ecology. His undergraduate research applied RAPD and RFLp to the study of genetic diversity in vineyard yeasts, and his graduate research from 1994 to 1998 has focused mainly on the interaction between amino acid and energy metabolism through molecular and genetic characterization of yeast’s resistance to 5,5,5 trifluoroleucine (TflR) as well as evolutionary analysis of the paralog gene families of histidine, leucine, and lysine biosynthesis. The genes conferring TflR resistance have also been used as dominant markers for the construction of plasmid vectors. From 1997 to 1999, Dr. Cavalieri has also contributed to the first European project using reverse genetic and phenotypic analysis of six new genes of S. cerevisiae chromosome IV (EU project EUROFAN). These studies have provided Dr. Cavalieri with a broad knowledge of central metabolism that is now fundamental for interpretation of genomic data.
In 1999 Cavalieri’s research addressed cloning and expression of ß-glucosidase gene from Debariomyces hansenii to enrich of wine with pharmacologically active resveratrol.
Curriculum Vitae, Duccio Cavalieri phD.
Researcher and Professor of Microbiology.
Current Address:Computational Biology
Research and Innovation Centre – Fondazione Edmund Mach
Via E. Mach 1, 38010 – S. Michele all’Adige (TN), Italia
Tel +39 0461 615 153
e-mail: duccio.cavalieri@iasma.it
Web Page:
http://www.duccioknights.org/
Appointments
- Harvard University Cambridge, MA, USA.Faculty of Arts and Sciences, Bauer Center for Genomics Research, CGR, Harvard Center for Systems Biology,2000-2004 Principal Investigator and Harvard Fellow, Group Leader of the “Yeast Population and Evolutionary Genomics Laboratory”
- University of Florence, Firenze, Fi, IT.Department of Pharmacology, 2004-2008 Ricercatore and Professore Aggregato of Microbiology
Education
- University of Florence, Firenze, Fi, IT. Biology 1993-1994 M.S. 1994
- University of Pavia, Pavia, Pv, IT. Genetics 1994-1998 Ph.D., 1998
- University of Florence, Firenze, Fi, IT Genetics Postdoctoral Fellow 1997-1998
- Consorzio Catania Ricerche, Catania, Post Doctoral Fellow, 1998-1999
- Harvard University Cambridge MA. USA Molecular Genetics and EvolutionPostdoctoral fellow 1999-2000
Grants and Funding
- 2010-2013 SYBARIS Network excellence EU grant.
- 2004-2009 NUGO (Nutrigenomics) Network of excellence EU grant.
- 2004-2009 DC-Thera Network of excellence EU grant.
- 2005-2008 Maths and Biology- EU grant.
- 2009-2010 PRIN-Italian Ministry of research grant.
- 2003-2005, National science foundation NSF grant 0313473, Division of Molecular and Cellular Biosciences.
- 2001-2004 Bauer Centre for Genomics Research, NIH Centre grant 2010 program, Harvard University, “Genomics Research Fellow” start-up grant.
- 2001-2002-Young investigator award grant, University of Florence.
Peer Reviewed publications on international journals
-Knowledge sharing and collaboration in translational research, and the DC-THERA Directory.
Splendiani A, Gündel M, Austyn JM, Cavalieri D, Scognamiglio C, Brandizi M.
Brief Bioinform. 2011 Oct 3. [Epub ahead of print] PMID:21969471 I.F 9.283
-Systems biology of infectious diseases: a focus on fungal infections.
Santamaría R, Rizzetto L, Bromley M, Zelante T, Lee W, Cavalieri D, Romani L, Miller B, Gut I, Santos M, Pierre P, Bowyer P, Kapushesky M.
Immunobiology. 2011 Nov;216(11):1212-27. PMID:21889228 I.F 4.114
-Friend or foe: using systems biology to elucidate interactions between fungi and their hosts.
Rizzetto L, Cavalieri D.
Trends Microbiol. 2011 Oct;19(10):509-15. PMID:21871806 I.F 7.500
-The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.
Beltrame L, Calura E, Popovici RR, Rizzetto L, Guedez DR, Donato M, Romualdi C, Draghici S, Cavalieri D.
Bioinformatics. 2011 Aug 1;27(15):2127-33. PMID:21653523 I.F 4.877
-The dectin-1/inflammasome pathway is responsible for the induction of protective T-helper 17 responses that discriminate between yeasts and hyphae of Candida albicans.
Cheng SC, van de Veerdonk FL, Lenardon M, Stoffels M, Plantinga T, Smeekens S, Rizzetto L, Mukaremera L, Preechasuth K, Cavalieri D, Kanneganti TD, van der Meer JW, Kullberg BJ, Joosten LA, Gow NA, Netea MG.
J Leukoc Biol. 2011 Aug;90(2):357-66. PMID:21531876 I.F 4.626
-Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: a retrospective study of two independent tumour tissue collections.
Marchini S, Cavalieri D, Fruscio R, Calura E, Garavaglia D, Nerini IF, Mangioni C, Cattoretti G, Clivio L, Beltrame L, Katsaros D, Scarampi L, Menato G, Perego P, Chiorino G, Buda A, Romualdi C, D’Incalci M.
Lancet Oncol. 2011 Mar;12(3):273-85. PMID:21345725 I.F 17.764
-DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.
Cavalieri D, Rivero D, Beltrame L, Buschow SI, Calura E, Rizzetto L, Gessani S, Gauzzi MC, Reith W, Baur A, Bonaiuti R, Brandizi M, De Filippo C, D’Oro U, Draghici S, Dunand-Sauthier I, Gatti E, Granucci F, Gündel M, Kramer M, Kuka M, Lanyi A, Melief CJ, van Montfoort N, Ostuni R, Pierre P, Popovici R, Rajnavolgyi E, Schierer S, Schuler G, Soumelis V, Splendiani A, Stefanini I, Torcia MG, Zanoni I, Zollinger R, Figdor CG, Austyn JM.
Immunome Res. 2010 Nov 19;6:10.PMID:21092113 I.F 5.33
-Chemical genetics approach to identify new small molecule modulators of cell growth by phenotypic screening of Saccharomyces cerevisiae strains with a library of morpholine-derived compounds.
Trabocchi A, Stefanini I, Morvillo M, Ciofi L, Cavalieri D, Guarna A.
Org Biomol Chem. 2010 Dec 21;8(24):5552-7. PMID:20949215 I.F 3.451
-Inhibition of immune synapse by altered dendritic cell actin distribution: a new pathway of mesenchymal stem cell immune regulation.
Aldinucci A, Rizzetto L, Pieri L, Nosi D, Romagnoli P, Biagioli T, Mazzanti B, Saccardi R, Beltrame L, Massacesi L, Cavalieri D, Ballerini C.
J Immunol. 2010 Nov 1;185(9):5102-10. PMID:20889545 I.F 5.745
-Evolution of transcriptional regulatory networks in yeast populations.
Cavalieri D.
Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun;2(3):324-35. PMID:20836032
-Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P.
Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6. PMID:20679230 I.F 9.771
-A systems biology approach to the mutual interaction between yeast and the immune system.
Rizzetto L, Cavalieri D.
Immunobiology. 2010 Sep-Oct;215(9-10):762-9. PMID:20646781 I.F 4.114
-A systems biology approach to dissection of the effects of small bicyclic peptidomimetics on a panel of Saccharomyces cerevisiae mutants.
Stefanini I, Trabocchi A, Marchi E, Guarna A, Cavalieri D.
J Biol Chem. 2010 Jul 23;285(30):23477-85. PMID:20501664 I.F 5.328
-Differential IL-17 production and mannan recognition contribute to fungal pathogenicity and commensalism.
Rizzetto L, Kuka M, De Filippo C, Cambi A, Netea MG, Beltrame L, Napolitani G, Torcia MG, D’Oro U, Cavalieri D.
J Immunol. 2010 Apr 15;184(8):4258-68. PMID:20228201 I.F 5.745
-Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level.
Buschow SI, Lasonder E, van Deutekom HW, Oud MM, Beltrame L, Huynen MA, de Vries IJ, Figdor CG, Cavalieri D.
J Proteome Res. 2010 Apr 5;9(4):1727-37.PMID:20131907 I.F 5.460
- Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.
Cavalieri D, Calura E, Romualdi C, Marchi E, Radonjic M, Van Ommen B, Müller M.
BMC Genomics. 2009 Dec 11;10:596.PMID: 20003344 IF 3.9
- Novel insights into phenotype and mitochondrial proteome of yeast mutants lacking proteins Sco1p or Sco2p. Gamberi T, Magherini F, Borro M, Gentile G, Cavalieri D, Marchi E, Modesti A.
Mitochondrion. 2009 Apr;9(2):103-14. Epub 2009 Jan 17.PMID: 19460303 IF 4.3
- Using pathway signatures as means of identifying similarities among microarray experiments.
Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L, Battaglia C, Cavalieri D.
PLoS One. 2009;4(1):e4128. Epub 2009 Jan 6.PMID: 19125200 IF 1.8
- Yeast as a model to investigate the mitochondrial role in adaptation to dietary fat and calorie surplus.
Marchi E, Cavalieri D. Genes Nutr. 2008 Dec;3(3-4):159-66. Epub 2008 Nov 27.PMID: 19037676 IF.1.8
- Biggeri A, Dreassi E, Lagazio C, Toti S, De Filippo C, Cavalieri D (2008) Hierarchical Bayesian Modelling of Multiple Arrays Experiments, BioMedical Statistics and Clinical Epidemiology, 2, 1, 47-55 (IF to be assigned).
- Ben van Ommen, Duccio Cavalieri, Helen Roche, Ulla Klein, Hannelore Daniel The challenges for molecular nutrition research 4: the “nutritional systems biology level”
Genes Nutr. 2008 Sep 30; : 18825427 (IF to be assigned).
- Kyle M. Brown, Christian R. Landry, Daniel L. Hartl and Duccio Cavalieri. Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Mol Ecol. 2008 Apr 17. IF=4.825
- Lotito L, Russo A, Chillemi G, Bueno S, Cavalieri D, Capranico G. Global Transcription Regulation by DNA Topoisomerase I in Exponentially Growing Saccharomyces cerevisiae Cells: Activation of Telomere-Proximal Genes by TOP1 Deletion. J Mol Biol. (2008) Jan 26; [Epub ahead of print] IF=4.890
- Cavalieri D, Dolara P., Mini.E., Luceri C., Maciag K., Toti S., Castagnini C., De Filippo C., Nobili S., Morganti M., Napoli C., Tonini G., Baccini M., Biggeri A., Tonelli F., Valanzano R., Orlando C., Gelmini S., Cianchi F., Messerini L., and Luzzatto L., Functional genomics approaches to unveil specific gene signatures as prognostic markers in sporadic colorectal cancer. Oncol Res. 2007;16(11):535-48.IF= 1.475.
- Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G, Queitsch C. Indel arrays: an affordable alternative for genotyping. Plant J. (2007) ;51(4):727-37. Epub 2007 Jul 20. IF= 6.565
- Cavalieri D., Castagnini C., Toti S., Maciag K., Kelder T., Gambineri P., Angioli S.and Dolara P. Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinformatics. 2007 Oct 1;23(19):2631-2. IF=4.894.
- Gamberi T., Cavalieri D., Magherini F., Mangoni M.L., De Filippo C., Borro M., Gentile G., Simmaco M., and Modesti A., An integrated analysis of the effects of Esculentin 1-21 on Saccharomyces cerevisiae. BBA – Proteins and Proteomics , Manuscript BBAPRO- Biochim Biophys Acta. 2007 Jun;1774(6):688-700. IF= 3.311
- Sardi I, Cavalieri D, Massimino M. Emerging treatments and gene expression profiling in high-risk medulloblastoma. Paediatr Drugs. 2007;9(2):81-96. Review. (IF to be assigned)
- Christian R. Landry, J.S. Oh, Daniel L. Hartl and Cavalieri D Transcriptional Plasticity in Saccharomyces cerevisiae: Variation and Constraints. Gene. 2006 Feb 1;366(2):343-51. Epub 2006 Jan 20. IF=2.721
- Christian R. Landry, Jeffrey P. Townsend, Daniel L. Hartl and Cavalieri D Ecological and Evolutionary Genomics of Saccharomyces cerevisiae (2006) Mol Ecol. 2006 Mar;15(3):575-91. IF=4.825
- Giuntini E., Mengoni A., De Filippo C., Cavalieri D., Aubin-Horth N., Landry C.R., Becker A, Bazzicalupo M.(2005) Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains BMC Genomics 2005, 6:158 doi:10.1186/1471-2164-6-158. IF= 4.029
- Cavalieri D., De Filippo C., Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug Disc Today 2005, 10:727-734. IF 10.8
- Luceri C, De Filippo C, Giovannelli L, Blangiardo M, Cavalieri D, Aglietti F, Pampaloni M, Andreuccetti D, Pieri L, Bambi F, Biggeri A and Dolara P. Extremely low frequency electromagnetic fields do not affect DNA damage and gene expression profiles of yeast and human lymphocytes. (2005) Radiation Research, 164, 277-285. IF=3.099
- Kandror O., Bretschneider N., Evgenj Kreydin, Cavalieri D., Goldberg A.L. (2004). Production of threalose and certain heat shock proteins occurs as part of a new adaptative response in yeast that enhances viability at 0 centigrades and upon freezing. Molecular Cell, 13, 771-781. IF=14.033.
- Cavalieri D, Grosu P.Integrating whole-genome expression results into metabolic networks with Pathway Processor. Curr Protoc Bioinformatics. 2004 May;Chapter 7:Unit 7.6
- Cavalieri D., P. McGovern, D. Hartl, R. Mortimer, M. Polsinelli. (2003) Evidence for S. cerevisiae fermentation in ancient wine. J. Mol. Evol, 57:S226-S232. IF= 2.767.
- Leung, JF., Cavalieri D., Fundamentals of Microarray Data Analysis, (2003). Trends in Genetics, 19 (11):649-659. IF=9.950
- Townsend, J.P., Cavalieri, D., Hartl, D.L. Population Genetic Variation in Global Gene Expression. (2003) Mol. Biol. Evol. 20: 955-963.IF= 6.726
- Cavalieri D, De Filippo C, Grosu P, and Biggeri A. (2002) Making sense of whole genome expression data: microarray databases and tools for integrating whole-genome expression results into cellular networks. Minerva Biotech, 14:291-304. IF= 0.396
- Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J. (2002) The underlying principles of scientific publication. Bioinformatics 18(11):1409. IF=4.894
- Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J. (2002) Standards for microarray data. Science. 298(5593):539. IF= 30.028.
- Sebastiani F., Barberio, C., Casalone, E., Cavalieri, D., Polsinelli, M. (2002) Crosses between Saccharomyces cerevisiae and Saccharomyces bayanus generate fertile hybrids. Res. Microbiol. Jan-Feb;153 (1):53-8. IF=2.504
- Grosu P., Townsend J.P., Hartl D.L., and Cavalieri D., Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Res. 2002 Jul;12(7):1121-6. if 10.256.
- Roselli G., Petruccelli R, Polsinelli L., Cavalieri D., (2002) Genetic Variability in Olea Europea sp. Journal of Genetics and Breeding Vol 56. IF=0.528
- Barberio C, Pagliai L, Cavalieri D, Fani R. (2001) Biodiversity and horizontal gene transfer in culturable bacteria isolated from activated sludge enriched in nonylphenol ethoxylates. Res Microbiol. Jan-Feb;152(1):105-12. IF=2.504
- Schaus SE, Cavalieri D, Myers AG. (2001) Gene transcription analysis of Saccharomyces cerevisiae exposed to neocarzinostatin protein- chromophore complex reveals evidence of DNA damage, a potential mechanism of resistance, and consequences of prolonged exposure Proc Natl Acad Sci U S A. Sep 25;98 (20):11075-80.IF=9.643
- Townsend, J.P., Cavalieri D., and D.L. Hartl, (2001). Population genomics: gene expression in a vineyard yeast from Tuscany. Biology International (International Union of Biological Societies) 41: 91-98. IF=0.213.
- De Filippo C and Cavalieri D., (2001) Yeast in the post genomic era: Use of DNA microarrays to study stress response, response to drugs and alkylating agents in S.cerevisiae. Minerva Biotech. v. 13(#4) pp. 249-254. . IF= 0.396
- Casalone, E., Barberio, C., Cavalieri, D., Polsinelli, M. (2000) Identification by functional analysis of the gene encoding alfa-isopropylmalate synthase II (LEU9) in Saccharomyces cerevisiae. Yeast (16):539-545. IF=1.955
- Cavalieri, D., Townsend, J. P. & Hartl, D. L. (2000) Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc Natl Acad Sci USA.; 97:12369-12374. IF= 9.643.
- Cavalieri D., C. Barberio ,E. Casalone, G.Fia, B. Bendoni e M. Polsinelli, (1999) Trifluoroleucine Resistance and regulation of alfa-isopropylmalate synthase I in Saccharomyces cerevisiae. Mol. Gen. Genet. 261: 152-160. IF=2.552
- Casalone, E., Barberio, C., Cavalieri, D., Ceccarelli, I, Riparbelli, M, Ugolini, S., Polsinelli, M. (1999) Disruption and phenotypic analysis of six novel genes from chromosome IV of Saccharomyces cerevisiae reveal ydl060w as an essential gene for vegetative growth. Yeast (15):1691-1701. IF=1.955
- Bendoni, B., Cavalieri, D., Casalone, E., Polsinelli, M. and Barberio, C. (1999) Trifluoroleucine resistance as a dominant molecular marker in transformation of wine natural strains of Saccharomyces cerevisiae. FEMS Microbiol Lett. 180(2):229-233. IF= 2.068.
- Cavalieri D., C. Barberio ,E. Casalone, F. Pinzauti, F. Sebastiani, R.K. Mortimer, M. Polsinelli. (1998) Genetic and molecular Diversity in S. cerevisiae natural populations. Food Technol. Biotechnol., 36 (1) 45-50. IF=0.789.
- R., Fani, E.Tamburini, E., Mori, A., Lazcano, P., Liò, C., Barberio, E., Casalone, D.,Cavalieri, B., Perito and M., Polsinelli (1997). Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces HIS6 and HIS7 genes. Gene, 197, 9-17. if=2.721.
- Casalone, E., Fia,G., Barberio, C., Cavalieri, D., Turbanti, L., Polsinelli, M. (1997) Genetic and Biochemical characterization of Saccharomyces cerevisiae mutants resistant to trifluoroleucine. Res. Microbiol., 1997, 148, 613-623. if= 2.504.
- D., Paffetti, C., Barberio, E., Casalone, D., Cavalieri, R., Fani, G., Fia, E., Mori, M., Polsinelli (1995), DNA fingerprinting by random amplified polymorphic DNA and restriction fragment length polymorphism are useful for yeast typing. Res. Microbiol., 146, 587-594. if=2.504.
- Bogani P., Cavalieri D., Petruccelli R., Polsinelli L., Roselli G. (1994), Identification of olive tree cultivars by using Random Amplified Polymorphic DNA. Acta Hort., 356, 98-101. if=0.179.
Publications in Books
1. Cavalieri D., De Filippo C., Lebboroni M., Rustioni M., Tuoni G., Ciofi D., Oliva G., Gargini A. e De Filippo G.B. (1997), Il fiume Pesa, la Fitodepurazione. Analisi integrata del Territorio. Comune di Tavarnelle Val di Pesa, pp1-158, Firenze, Settembre 1997.
2. Mario Polsinelli, Claudia Barberio, Enrico Casalone, Duccio Cavalieri. (1998) Le tecnologie biomolecolari nello studio della biodiversità dei lieviti. I Georgofili, Quaderni 1998-VII, 37-64.
3. Duccio Cavalieri (2000) La Variabilità in popolazioni naturali di lieviti da vino. (Variability in natural populations of wine yeasts) In “I nostri Lieviti dalla vite al vino”, pag 50-62, Aida edizioni, luglio 2000.
4. Yeffrey Townsend and Duccio Cavalieri Cover Page Image, and paragraph 13.8 page 578-580 Functional Genomics in Chapter 13 Genetic Ingeneering and Genomics, in Genetics-Analysis of Genes and Genomes from DL Hartl and EW Jones, 2001, Jones and Bartlett Publishers Sudbury MA.
5. Hartl, D.L., C.D. Meiklejohn, C.I. Castillo-Davis, D. Cavalieri, J.M. Ranz, and J.P. Townsend, (2003). Expression Profiling in Evolutionary Genetics. In The Evolution of Population Biology: Modern Synthesis, pp74-93 Eds. R. K. Singh and M. K. Uyenoyama. Cambridge University Press, Cambridge.
6. Duccio Cavalieri e Carlotta De Filippo, Metodi di analisi con microarrays, in Benedetti A., Mocali S., Miclaus N.(Ed.): Manuale di metodi innovativi per lo studio dei microrganismi del suolo. Collana SISS sui Metodi di Analisi del Suolo, Franco Angeli editore, Milano. 2008.
7. Biggeri A, Cavalieri D, Dreassi E, Lagazio C, Toti S (2004) Hierarchical Bayesian Modelling of Multiple Arrays Experiments, Note di ricerca del Dipartimento di Statistica dell’Università di Udine, 11.04.
8. Duccio Cavalieri, (1998) tesi di Dottorato di Ricerca in Scienze Genetiche (Genetica e Biologia Molecolare) X ciclo, “Isolamento e caratterizzazione genetico-molecolare di mutanti di Saccharomyces cerevisiae resistenti alla 5,5,5-trifluoro-DL leucina e identificazione del gene codificante l’-isopropil-malato sintetasi II” febbraio 1998. Biblioteca del dipartimento di Genetica di Pavia, Biblioteca del dipartimento di Biologia Animale e Genetica di Firenze, Biblioteca Nazionale Centrale di Roma e Firenze.
Peer Reviewed Publications of Proceedings of International Conferences in international journals.
1. Casalone, E., Barberio, B. Bendoni, D. Cavalieri, A.Pace, M. Polsinelli (1999) Role of -IPMS I in the regulation of mitochondrial metabolism in Saccharomyces cerevisiae. XIX International Conference on Yeast Genetics and Molecular Biology Rimini, Italy, 25-30/5/1999. Curr. Genet. 35, (3) 279.
2. Cavalieri D., Townsend J., Polsinelli M., Hartl D.L., Whole genome expression analysis of colony morphology in vineyard isolates of S.cerevisiae. XX International Conference on Yeast Genetics and Molecular Biology, Prague, 10-11-9-2001. Yeast 2001;18:S 110.
3. De Filippo C., Cavalieri D., Jelinsky S., Dolara P., Samson L., Global expression analysis of anaerobically growing cells of S.cerevisiae treated with methyl methansulfonate, XX International Conference on Yeast Genetics and Molecular Biology, Prague, 10-11-9-2001. Yeast 2001;18:S 194.
4. Duccio Cavalieri, Julia Oh, Christine Queitsch, Christian Landry. Transcriptional analysis of coexisting genomes in interspecific hybrids of Saccharomyces cerevisiae and Saccharomyces bayanus. Yeast 2005;22:S36_1.16.
5. Julia Oh, Duccio Cavalieri. Everything you always wanted to know about wine yeasts but were afraid to ask.. Yeast 2005;22:S117_8.3.
6. Biggeri A., Toti S., Dreassi E., Lagazio C., Gasparini M., DeFilippo C., Morneau K.,
7. Bergerat A., and Cavalieri D., “A Hierarchical Bayesian model to study temperature-dependent variation of sequence-specific hybridization to cDNA Microarray” Workshop on Statistical Analysis of Gene expression data, Proceedings of The Royal Statistical Society, Wye, UK, 11-14 July 2003 (11-2).
Selected Invited Lectures.
1. 25/08/1997 Cavalieri D, Genetic and molecular diversity in Saccharomyces cerevisiae natural population. International Specialised Symposium on Yeast” Bled, Slovenia 24th – 29th/08/1997.
2. 15/6/2002 Cavalieri, D., Keynote Lecture Evolutionary Genomics of Natural Populations of S. cerevisiae, atti del congresso “Molecular Evolution”., Sorrento, Napoli 13-16/6/2002.
3. 13-15/10/2004 D. Cavalieri. Ricostruzione di reti di regolazione attraverso l’integrazione dell’espressione genomica globale in pathway cellulari. 7° Congresso Nazionale Società di Genetica Umana, Pisa.
4. 21/05/04 Seminario-“La Bioinformatica nella ricerca e nello sviluppo Industriale”. Giornata Ufficiale di Presentazione di Proteo Gen Bio S.r.L. Spin-Off dell’università di Pisa. Dipartimento di Informatica, Pisa.
5. 1/06/2004 D. Cavalieri, “DNA microarrays in population genetics”, meeting “DNA microarrays”, Milano, Centro Lita, CNR, acts published on Minerva Biotecnologica.
6. 27/05/2004, D.Cavalieri, Dipartimento di Scienze Biochimiche, Universita’ di Bari, PhD school lesson and lecture, “Dalla Genomica Funzionale alla Systems Biology”.
7. 13/03/2004 D.Cavalieri. “Evolution of regulatory networks in natural populations of S.cerevisiae”
8. Symposium on The Evolution of Gene Regulation, IGERT, Eugene Oregon, “Evolutionary and environmental genomics of yeast”.
9. 8-10/09/2004 D. Cavalieri. “Pathway Based Analysis of Microarray Data”, 1st Nutrigenomics Conference European Nutrigenomics Organization, , Wageningen, The Netherlands.
10. 12 /11/2004: Department of Genetics, Leicester University (UK) invited lecture “Structural and functional variation in S.cerevisiae populations on a genome scale”.
11. 16/12/2004 Christmas lecture: Keynote speaker, ’NIEHS, Research Triangle Park, North Carolina (USA) “Genetic variation in the transcriptional and metabolic plasticity of yeast responses to toxicants”.
12. 27-29/01/2005. D. Cavalieri. “Progress in Pathway based analysis of nutrigenomics data”. NuGo meeting, Monaco, Germania.
13. 13/05/2005, Duccio Cavalieri-Pathway based microarray data analysis. Workshop “Satellite Pathway discovery and analysis”, international workshop “Functional genomics principles of statistics and genomics”-San Domenico, Firenze 9-13 maggio 2005.
14. 17/03/2005 Duccio Cavalieri Invited Lecture Center for Clinical and Scientific Research, Stanford University, Stanford, CA (USA) “Genetic variation for phenotypic plasticity”.
15. 22/08/05: Duccio Cavalieri. Everything you always wanted to know about wine yeasts but were afraid to ask. XXII International Conference on Yeast Genetics and Molecular Biology, Bratislava.
16. 12/09/05 Cavalieri D., S.cerevisiae as a model in nutritional systems biology. Second European Nutrigenomics Conference. International Conference Center Il Ciocco, Book of Abstracts.
17. 13/05/05; Cavalieri D. Pathway analysis and statistics. Functional Genomics: Principles of Statistics and Biology course. Florence.
18. 12/09/05 Speaker, Organizer and Chair, “A Pathway logic to genomics”, NuGO workshop “Pathway analysis and genome wide expression sets”. Chris Evelo and Duccio Cavalieri workshop organizers. Organised during the Second European Nutrigenomics Conference, September 12 2005, Castelvecchio Pascoli, Tuscany, Italy.
19. 22/07/2006 Duccio Cavalieri-“Functional Genomics Approaches to discovery of prognostic markers in colon cancer patients”. Saturday -Certosa di Pontignano Siena, First Annual Scientific Conference of Istituto Toscano Tumori (ITT)
20. 22/09/2006 Duccio Cavalieri, Seminario “Approcci di Genomica Funzionale allo sviluppo di nuovi marcatori prognostici” Istituto Giannina Gaslini, Genova.
21. 15/09/06 Duccio Cavalieri, Eugene a Bioinformatics tool for pathway based analysis of nutrigenomics data. Third European Nutrigenomics Conference 12-15 september 2006 Keble College Oxford UK Book of abstract p. 42.
22. 11/05/2007, Bioinformatic Methods for Pathway Based Analysis of genomics data: A comparative Analysis. Debrecen, Hungary, Mini Symposium on Stem Cells and Immunity.
23. 05/09/2007, Duccio Cavalieri “A mitochondrial perspective to comparative nutritional systems Biology”, Fourth European Nutrigenomics Conference OSLO 2007.
24. 20/11/2007 Duccio Cavalieri, Chair-Session Phenotypic Analysis of Eukaryotes: Florence Conference on Phenotype Microarray Analysis of Microorganisms, The environment, Agriculture and Human Health, Firenze, Italy, March 19-21-2008.
25. 14-16/04/08. Duccio Cavalieri, Organizer, Chair and Speaker, Fifth DC-Thera Meeting Athens, EuGene a method for Pathway Based Analysis and Representation for the Dendritic Cell.
26. 5/07/2008, Duccio Cavalieri-“From Genomics data to cancer cell Biology”. Palazzo dei Congressi Firenze, International Symposium on “Cancer genotypes, Cancer phenotypes” Chair Silvio Garattini, Organizer Lucio Luzzatto, Istituto Toscano Tumori (ITT).
27. 5/09/08, Duccio Cavalieri, Comparative Nutritional Systems Biology-Fifth European Nutrigenomics Conference, September 2-5 2008, Potsdam, Germany.
28. 2/09/08, Duccio Cavalieri, Evolution of transcriptional regulatory networks in yeast populations Riva del Garda, Italy International Meeting “Microarray and Gene Expression Data Society”1-4/09/08.
29. 25/09/08, D. Cavalieri Pathway analysis, an overview, and Chair Parallel Workshop, Bioinformatics and Genomics, FISV 2008 X annual congress 24-25 September 2008.
30. 2/10/08, Duccio Cavalieri, An ecological perspective to the investigation of the Evolution and Variation of the yeast transcriptome. EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts, EMBL Heidelberg, 1-5 October 2008.
31. 14-16/11/08. Duccio Cavalieri, Organizer, Chair and Speaker, International Workshop on Gene Signalling Pathway Analysis and Representation for the Dendritic Cell.
Teaching activities.
26 January 2005: Lezione presso il Corso di Master in NBC- Accademia Militare di Sanità, titolo “Metodi di identificazione e difesa da microrganismi patogeni, epidemie e bioterrorismo”.
28 January 2006: Lezione presso il Corso di Master in NBC- Accademia Militare di Sanità, titolo “Metodi di identificazione e difesa da microrganismi patogeni, epidemie e bioterrorismo”.
4 February 2007: Lezione presso il Corso di Master in NBC- Accademia Militare di Sanità, titolo “Metodi di identificazione e difesa da microrganismi patogeni, epidemie e bioterrorismo”.
7 february 2005: Invited lecturer, Scuola di Dottorato di Ricerca dell’Università degli Studi di Torino “Microarrays in population genetics” and “Yeast Genomics as a model to study human Tfs, the p53 test case”.
18 february 2005: Lecture: Pathway based analysis of microarray data, EMBO Practical Course on Functional Genomics, Milano Bicocca.
Duccio Cavalieri-Lcture “La genomica funzionale e principi di regolazione della trascrizione”. Corso internazionale, Functional genomics principles of statistics and genomics-San Domenico, Firenze 9-13 maggio 2005.
Academic Year 2003-2004 Laboratorio di Microbiologia (2 crediti), Corso di Laurea in Biotecnologie, Università degli Studi di Firenze.
Academic Year 2004-2005, Microbiologia Generale, Corso di Laurea in Biotecnologie, 5 credits total 45 hours of lectures.
Academic Year 2006-2007, Microbiologia Generale, Corso di Laurea in Biotecnologie, 5 credits total 45 hours of lectures.
Academic Year 2007-2008, Microbiologia Generale, Corso di Laurea in Biotecnologie, 5 credits total 45 hours of lectures.
Academic Year 2007-2008, Microbiologia Generale, Corso di Laurea in Chimica e Tecnologie Farmaceutiche, 5 credits total 45 hours of lectures.
